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    stpA DNA-binding transcriptional repressor StpA with RNA chaperone activity [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 947130, updated on 27-Nov-2023

    Summary

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    Gene symbol
    stpA
    Gene description
    DNA-binding transcriptional repressor StpA with RNA chaperone activity
    Primary source
    ASAP:ABE-0008788
    Locus tag
    b2669
    See related
    ECOCYC:EG11554
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Escherichia coli str. K-12 substr. MG1655 (strain: K-12, substrain: MG1655)
    Lineage
    Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia
    Also known as
    ECK2663; hnsB
    Summary
    StpA binds prefereably unstructured RNA weakly, with mainly electrostatic interactions that promote RNA folding (Mayer, 2007). [More information is available at EcoGene: EG11554]. StpA is a DNA-binding protein with similarity to H-NS. [More information is available at EcoCyc: EG11554].
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    Genomic context

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    Sequence:
    NC_000913.3 (2798091..2798495, complement)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene putative DNA-binding transcriptional regulator YgaV Neighboring gene thiosulfate sulfurtransferase YgaP Neighboring gene L-alanine exporter Neighboring gene DUF2002 domain-containing protein YgaC

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_000913.3

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. The RNA chaperone StpA enables fast RNA refolding by destabilization of mutually exclusive base pairs within competing secondary structure elements. Hohmann KF, et al. Nucleic Acids Res, 2021 Nov 8. PMID 34614185, Free PMC Article
    2. StpA represses CRISPR-Cas immunity in H-NS deficient Escherichia coli. Mitić D, et al. Biochimie, 2020 Jul. PMID 32353388
    3. Gene silencing H-NS paralogue StpA forms a rigid protein filament along DNA that blocks DNA accessibility. Lim CJ, et al. Nucleic Acids Res, 2012 Apr. PMID 22187157, Free PMC Article
    4. RNA chaperone activity and RNA-binding properties of the E. coli protein StpA. Mayer O, et al. Nucleic Acids Res, 2007. PMID 17267410, Free PMC Article
    5. StpA protein from Escherichia coli condenses supercoiled DNA in preference to linear DNA and protects it from digestion by DNase I and EcoKI. Keatch SA, et al. Nucleic Acids Res, 2005. PMID 16299353, Free PMC Article

    See all (63) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. RfaH Counter-Silences Inhibition of Transcript Elongation by H-NS-StpA Nucleoprotein Filaments in Pathogenic Escherichia coli.
      Title: RfaH Counter-Silences Inhibition of Transcript Elongation by H-NS-StpA Nucleoprotein Filaments in Pathogenic Escherichia coli.
    2. The RNA chaperone StpA enables fast RNA refolding by destabilization of mutually exclusive base pairs within competing secondary structure elements.
      Title: The RNA chaperone StpA enables fast RNA refolding by destabilization of mutually exclusive base pairs within competing secondary structure elements.
    3. StpA represses CRISPR-Cas immunity in H-NS deficient Escherichia coli.
      Title: StpA represses CRISPR-Cas immunity in H-NS deficient Escherichia coli.
    4. Hha and StpA greatly enhance H-NS-stimulated pausing by RNAP at 20 degrees C. StpA:H-NS or StpA-only filaments also stimulate pausing at 37 degrees C, a temperature at which Hha:H-NS or H-NS-only filaments have much less effect. In addition, both Hha and StpA greatly stimulate DNA-DNA bridging by H-NS filaments.
      Title: StpA and Hha stimulate pausing by RNA polymerase by promoting DNA-DNA bridging of H-NS filaments.
    5. three new candidates of E. coli nucleoid, namely DNA-binding protein from starved cells (Dps), host factor for phage Qbeta (Hfq) and suppressor of td(-) phenotype A (StpA)
      Title: Growth phase dependent changes in the structure and protein composition of nucleoid in Escherichia coli.
    6. Also, DeltahnsDeltastpA double mutants simultaneously lacking H-NS and its paralog StpA showed more severe reductions in ompW expression at 37 degrees C, resulting in the complete loss of OmpW.
      Title: Expression of the Escherichia coli ompW colicin S4 receptor gene is regulated by temperature and modulated by the H-NS and StpA nucleoid-associated proteins.
    7. Both the DNA binding sites of H-NS as well as the function of StpA as a backup system might be selected for silencing highly transcribable genes.
      Title: Genomic analysis reveals epistatic silencing of "expensive" genes in Escherichia coli K-12.
    8. In contrast to H-NS, the StpA filament interacts with a naked DNA segment to cause DNA bridging which results in simultaneous stiffening and bridging of DNA.
      Title: Gene silencing H-NS paralogue StpA forms a rigid protein filament along DNA that blocks DNA accessibility.
    9. StpA binding profile reduced to one-third in the hns mutant and the H-NS binding profile was unaffected by stpA inactivation.
      Title: Differential binding profiles of StpA in wild-type and h-ns mutant cells: a comparative analysis of cooperative partners by chromatin immunoprecipitation-microarray analysis.
    10. StpA in homologous recombination and double-strand break repair is discussed
      Title: Roles of the DNA binding proteins H-NS and StpA in homologous recombination and repair of bleomycin-induced damage in Escherichia coli.
    Submit: New GeneRIF Correction See all GeneRIFs (17)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Gene Ontology Provided by EcoCyc

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-binding transcription repressor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables bent DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables minor groove of adenine-thymine-rich DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein dimerization activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables structural constituent of chromatin IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transcription cis-regulatory region binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoid IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of protein-DNA complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    DNA-binding transcriptional repressor StpA with RNA chaperone activity

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_000913.3 Reference assembly

      Range
      2798091..2798495 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_417155.1 DNA-binding transcriptional repressor StpA with RNA chaperone activity [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_417155.1

      Status: PROVISIONAL

      UniProtKB/TrEMBL
      A0A5B9APP6, A0A826PC59
      Conserved Domains (1) summary
      PRK10328
      Location:1 → 134
      PRK10328; DNA-binding protein StpA
    Nucleotide Protein
    Heading Accession and Version

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